Phylogeny with a multiprosessor?

Hi there
very soon we'll have a fully operational Linux-Pentium-cluster, and I
just got the idea to run some phylogeny searches on it. I wonder if the
full capacity of a multiprosessor computer can be used by common
phylogeny programs.
We have some Pentium two-CPU-computers and additional
single-CPU-computers, and all of them will be in the network. At the
moment I'm just running MOLPHY but I'd also like to test PAML and, of
course, PAUP, if it will ever be available for Pentium-Linux. Are these
programs able to use the full capacity of a multiprosessor
Pentium-computer? Is it tricky thing to make it? Especially PAUP is
interesting, as we have no real reason to buy a UNIX-version of it,
unless it would be considerably faster on the cluster than on a Macintosh.
Thanks for your help!
Ari